Cerulean: A hybrid assembly using high throughput short and long reads

Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking regions. The emergence of third generation sequencing (Pacific Biosciences) with long reads enables the opportunity to resolve complicated repeats that could not be resolved by the short read data. However, these long reads have high error rate and it is an uphill task to assemble the genome without using additional high quality short reads. Recently, Koren et al. 2012 proposed an approach to use high quality short reads data to correct these long reads and, thus, make the assembly from long reads possible. However, due to the large size of both dataset (short and long reads), error-correction of these long reads requires excessively high computational resources, even on small bacterial genomes. In this work, instead of error correction of long reads, we first assemble the short reads and later map these long reads on the assembly graph to resolve repeats. Contribution: We present a hybrid assembly approach that is both computationally effective and produces high quality assemblies. Our algorithm first operates with a simplified version of the assembly graph consisting only of long contigs and gradually improves the assembly by adding smaller contigs in each iteration. In contrast to the state-of-the-art long reads error correction technique, which requires high computational resources and long running time on a supercomputer even for bacterial genome datasets, our software can produce comparable assembly using only a standard desktop in a short running time.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Four methods for determining the composition of trace radioactive surface contamination of low-radioactivity metal

Four methods for determining the composition of low-level uranium- and thorium-chain surface contamination are presented. One method is the observation of Cherenkov light production in water. In two additional methods a position-sensitive proportional counter surrounding the surface is used to make both a measurement of the energy spectrum of alpha particle emissions and also coincidence measurements to derive the thorium-chain content based on the presence of short-lived isotopes in that decay chain. The fourth method is a radiochemical technique in which the surface is eluted with a weak acid, the eluate is concentrated, added to liquid scintillator and assayed by recording beta-alpha coincidences. These methods were used to characterize two `hotspots' on the outer surface of one of the He-3 proportional counters in the Neutral Current Detection array of the Sudbury Neutrino Observatory experiment. The methods have similar sensitivities, of order tens of ng, to both thorium- and uranium-chain contamination.Comment: 22 pages, 19 figure

Vertical distribution and migration of fish larvae in the NW Iberian upwelling system during the winter mixing period: implications for cross-shelf distribution

The vertical distribution and vertical migrations of fish larvae and implications for their cross-shelf distribution were investigated in the northern limit of the NE Atlantic upwelling region during the late winter mixing period of 2012. The average positive values of the upwelling index for February and March of this year were far from normal, although the average hydrographic conditions during the period of study were of downwelling and the water column was completely mixed. Fish larvae, most in the preflexion stage, were concentrated in the upper layers of the water column and their distribution was depth stratified, both day and night. However, the larval fish community was not structured in the vertical plane and fish larvae did not show significant diel vertical migration (DVM), although five species showed ontogenetic vertical migration. In regions of coastal upwelling and in the absence of DVM, the location of fish larvae in the water column is crucial for their cross-shelf distribution. Thus, the cross-shelf distribution of the six most abundant species collected in this study can be explained by the surface onshore flow associated with coastal downwelling, retaining larvae of the coastal spawning species with a relatively shallow distribution in the shelf region and transporting larvae of slope spawning species onto the shelf. The wide vertical distribution shown by larvae of the offshore spawning species could be an adaptation of these species to ensure that some larvae reach the inshore nursery areasPlan Nacional de I+D+i (CRAMERCTM2010- 21856-CO3-02), Junta de Galicia (ECOPREGA-10MMA602021PR), Principado de Asturias (GRUPIN14-144)Postprint2,044

Microcausality and quantization of the fermionic Myers-Pospelov model

We study the fermionic sector of the Myers and Pospelov theory with a general background $n$. The spacelike case without temporal component is well defined and no new ingredients came about, apart from the explicit Lorentz invariance violation. The lightlike case is ill defined and physically discarded. However, the other case where a nonvanishing temporal component of the background is present, the theory is physically consistent. We show that new modes appear as a consequence of higher time derivatives. We quantize the timelike theory and calculate the microcausality violation which turns out to occur near the light cone.Comment: 9 pages and 3 figures, new version accepted in EPJC, Volume 72, Issue 9, includes lee-wick review, microcausalit

Detector Description and Performance for the First Coincidence Observations between LIGO and GEO

For 17 days in August and September 2002, the LIGO and GEO interferometer gravitational wave detectors were operated in coincidence to produce their first data for scientific analysis. Although the detectors were still far from their design sensitivity levels, the data can be used to place better upper limits on the flux of gravitational waves incident on the earth than previous direct measurements. This paper describes the instruments and the data in some detail, as a companion to analysis papers based on the first data.Comment: 41 pages, 9 figures 17 Sept 03: author list amended, minor editorial change

Size Doesn't Matter: Towards a More Inclusive Philosophy of Biology

notes: As the primary author, O’Malley drafted the paper, and gathered and analysed data (scientific papers and talks). Conceptual analysis was conducted by both authors.publication-status: Publishedtypes: ArticlePhilosophers of biology, along with everyone else, generally perceive life to fall into two broad categories, the microbes and macrobes, and then pay most of their attention to the latter. ‘Macrobe’ is the word we propose for larger life forms, and we use it as part of an argument for microbial equality. We suggest that taking more notice of microbes – the dominant life form on the planet, both now and throughout evolutionary history – will transform some of the philosophy of biology’s standard ideas on ontology, evolution, taxonomy and biodiversity. We set out a number of recent developments in microbiology – including biofilm formation, chemotaxis, quorum sensing and gene transfer – that highlight microbial capacities for cooperation and communication and break down conventional thinking that microbes are solely or primarily single-celled organisms. These insights also bring new perspectives to the levels of selection debate, as well as to discussions of the evolution and nature of multicellularity, and to neo-Darwinian understandings of evolutionary mechanisms. We show how these revisions lead to further complications for microbial classification and the philosophies of systematics and biodiversity. Incorporating microbial insights into the philosophy of biology will challenge many of its assumptions, but also give greater scope and depth to its investigations

Genome-wide meta-analysis uncovers novel loci influencing circulating leptin levels.

Leptin is an adipocyte-secreted hormone, the circulating levels of which correlate closely with overall adiposity. Although rare mutations in the leptin (LEP) gene are well known to cause leptin deficiency and severe obesity, no common loci regulating circulating leptin levels have been uncovered. Therefore, we performed a genome-wide association study (GWAS) of circulating leptin levels from 32,161 individuals and followed up loci reaching P<10(-6) in 19,979 additional individuals. We identify five loci robustly associated (P<5 × 10(-8)) with leptin levels in/near LEP, SLC32A1, GCKR, CCNL1 and FTO. Although the association of the FTO obesity locus with leptin levels is abolished by adjustment for BMI, associations of the four other loci are independent of adiposity. The GCKR locus was found associated with multiple metabolic traits in previous GWAS and the CCNL1 locus with birth weight. Knockdown experiments in mouse adipose tissue explants show convincing evidence for adipogenin, a regulator of adipocyte differentiation, as the novel causal gene in the SLC32A1 locus influencing leptin levels. Our findings provide novel insights into the regulation of leptin production by adipose tissue and open new avenues for examining the influence of variation in leptin levels on adiposity and metabolic health

The Sudbury Neutrino Observatory

The Sudbury Neutrino Observatory is a second generation water Cherenkov detector designed to determine whether the currently observed solar neutrino deficit is a result of neutrino oscillations. The detector is unique in its use of D2O as a detection medium, permitting it to make a solar model-independent test of the neutrino oscillation hypothesis by comparison of the charged- and neutral-current interaction rates. In this paper the physical properties, construction, and preliminary operation of the Sudbury Neutrino Observatory are described. Data and predicted operating parameters are provided whenever possible.Comment: 58 pages, 12 figures, submitted to Nucl. Inst. Meth. Uses elsart and epsf style files. For additional information about SNO see http://www.sno.phy.queensu.ca . This version has some new reference

The design, construction, and commissioning of the KATRIN experiment

The KArlsruhe TRItium Neutrino (KATRIN) experiment, which aims to make a direct and model-independent determination of the absolute neutrino mass scale, is a complex experiment with many components. More than 15 years ago, we published a technical design report (TDR) [1] to describe the hardware design and requirements to achieve our sensitivity goal of 0.2 eV at 90% C.L. on the neutrino mass. Since then there has been considerable progress, culminating in the publication of first neutrino mass results with the entire beamline operating [2]. In this paper, we document the current state of all completed beamline components (as of the first neutrino mass measurement campaign), demonstrate our ability to reliably and stably control them over long times, and present details on their respective commissioning campaigns